Using populations of beads for the fabrication of arrays on surfaces

Abstract

The present invention provides methods for creating an array of features on a surface based on content transferred from a plurality of beads to the surface. Nucleic acid content can be transferred using a method including the steps of (a) providing a surface having one or more primer oligonucleotides attached to the surface; (b) providing a pool of beads, wherein beads in the pool have a plurality of templates attached thereto, the plurality comprising multiple copies of a single nucleic acid template sequence; (c) arraying the beads onto the surface by hybridizing the templates to the primer oligonucleotides; and (d) extending the primers to produce copies of the templates attached to the surface.

The invention claimed is: 
     
       1. An array comprising spatially discrete nucleic acid features on a surface, wherein each spatially discrete feature comprises two or more different amplification primers each having a different sequence attached to the surface, and wherein each spatially discrete feature is separated from any other discrete feature by a space which does not carry amplification primers, wherein the array of spatially discrete features comprises an average center-to-center distance that is less than two times the diameter of a feature. 
     
     
       2. The array of  claim 1 , wherein the surface is flat or planar. 
     
     
       3. The array of  claim 1 , wherein the surface comprises wells, depressions, pillars, ridges or channels. 
     
     
       4. The array of  claim 1 , wherein the surface comprises a hydrogel. 
     
     
       5. The array of  claim 1 , wherein the array further comprises amplified nucleic acids. 
     
     
       6. The array of  claim 1 , wherein the spatially discrete nucleic acid features on the surface are of similar size to each other. 
     
     
       7. The array of  claim 1 , wherein the array is fabricated by a method comprising:
 (a) providing a plurality of beads, wherein each bead in the plurality of beads comprises nucleic acid content comprising two or more different amplification primers each having a different sequence; 
 (b) contacting the plurality of beads with a surface to produce a layer of beads on the surface, wherein the layer of beads comprises an average center-to-center distance that is less than two times the diameter of a bead; 
 (c) transferring the nucleic acid content from the beads to the surface to create an array of spatially discrete features on the surface, wherein each spatially discrete feature comprises nucleic acid content from a bead in the plurality of beads, the nucleic acid content comprising amplification primers and wherein each spatially discrete feature on the array is separated from any other discrete feature by a space which does not carry amplification primers; 
 (d) removing the plurality of beads from the surface. 
 
     
     
       8. The array of  claim 7 , wherein the array of spatially discrete features comprises an average center-to-center spacing that is equivalent to the diameter of the beads. 
     
     
       9. A method of creating an array comprising spatially discrete nucleic acid features on a surface, wherein each spatially discrete feature comprises two or more different amplification primers each having a different sequence attached to the surface, and wherein each spatially discrete is separated from any other discrete feature by a space which does not carry amplification primers, the method comprising:
 (a) providing a plurality of beads, wherein each bead in the plurality of beads comprises nucleic acid content comprising two or more different amplification primers each having a different sequence; 
 (b) contacting the plurality of beads with a surface to produce a layer of beads on the surface, wherein the layer of beads comprises an average center-to-center distance that is less than two times the diameter of a bead; 
 (c) transferring the nucleic acid content from the beads to the surface to create an array of spatially discrete features on the surface, wherein each spatially discrete feature comprises nucleic acid content from a bead in the plurality of beads, the nucleic acid content comprising amplification primers and wherein each spatially discrete feature on the array is separated from any other discrete feature by a space which does not carry amplification primers; 
 (d) removing the plurality of beads from the surface. 
 
     
     
       10. The method of  claim 9 , wherein the transferring of the nucleic acid content comprises physically transferring nucleic acids from each of the beads to attach the nucleic acids to a feature on the surface. 
     
     
       11. The method of  claim 9 , wherein the transferring comprises covalently attaching the nucleic acid content from the beads to each of the spatially discrete features on the surface. 
     
     
       12. The method of  claim 9 , wherein the transferring comprises non-covalently attaching the nucleic acid content from the beads to each of the spatially discrete features on the surface. 
     
     
       13. The method of  claim 9 , wherein the transferring of the nucleic acids comprises replicating a nucleic acid from each of the beads to form a copy of the nucleic acid at each of the spatially discrete features. 
     
     
       14. The method of  claim 9 , wherein the transferring of the nucleic acids comprises physically transferring a nucleic acid molecule from each of the beads to attach the nucleic acid molecule to each of the spatially discrete features. 
     
     
       15. The method of  claim 9 , wherein the nucleic acids that are transferred from the beads to the surface are single stranded. 
     
     
       16. The method of  claim 9 , wherein the array of spatially discrete features comprises an average center-to-center spacing that is equivalent to the diameter of the beads. 
     
     
       17. The method of  claim 9 , wherein the surface is flat or planar. 
     
     
       18. The method of  claim 9 , wherein the surface comprises wells, depressions, pillars, ridges or channels. 
     
     
       19. The array of  claim 1 , wherein at least one or more of the amplification primers comprise the sequence set forth in one or more of SEQ ID NOs: 1-4. 
     
     
       20. The method of  claim 9 , wherein at least one or more of the amplification primers comprise the sequence set forth in one or more of SEQ ID NOs: 1-4.